Ground state#
import veloxchem as vlx
The initial structure can e.g. be defined in terms of a SMILES string.
molecule = vlx.Molecule.read_smiles("OC=CC=O")
molecule.show()
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jupyter labextension install jupyterlab_3dmol
Define the electronic structure theory method.
scf_drv = vlx.XtbDriver()
Optimize the molecule structure with the OptimizationDriver class in VeloxChem.
opt_drv = vlx.OptimizationDriver(scf_drv)
opt_drv.ostream.mute()
opt_results = opt_drv.compute(molecule)
The SCF energies calculated in the optimization process are available in the resulting object.
from matplotlib import pyplot as plt
e_min_in_au = min(opt_results["opt_energies"])
energies_in_kcalpermol = [
(e - e_min_in_au) * vlx.hartree_in_kcalpermol() for e in opt_results["opt_energies"]
]
fig, ax = plt.subplots(figsize=(6, 3))
ax.plot(energies_in_kcalpermol, "o--")
ax.set_xlabel("Iteration")
ax.set_ylabel(r"Energy relaxation (kcal/mol)")
plt.show()
The molecular structure relaxation can be visualized.
import py3Dmol as p3d
viewer = p3d.view(width=400, height=300)
viewer.addModelsAsFrames("".join(opt_results["opt_geometries"]))
viewer.animate({"loop": "forward"})
viewer.setViewStyle({"style": "outline", "width": 0.05})
viewer.setStyle({"stick": {}, "sphere": {"scale": 0.25}})
viewer.zoomTo()
viewer.show()
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jupyter labextension install jupyterlab_3dmol
Larger molecules#
Cafestol and kahweol are molecules present in Robusta and Arabica coffee beans, respectively.
We here use the semi-empirical tight binding method named xTB and a code implementation that has been interfaced to VeloxChem.
Show code cell source
cafestol_xyz = """51
cafestol initial structure
O -4.5215 -1.3455 0.4926
O -5.2905 0.0812 -1.7033
O 5.1630 0.4345 -0.1101
C -1.2807 -0.7511 -0.0465
C -0.5244 0.5810 -0.4102
C 0.9909 0.6610 0.0407
C -2.9440 0.2916 1.2866
C -1.8143 -0.7311 1.3945
C -2.6188 -0.8159 -0.8642
C -3.7116 -0.2387 0.0606
C -0.4332 -2.0024 -0.3283
C -1.3742 1.8303 -0.0654
C 1.6844 -0.6873 -0.4019
C -2.3206 1.6833 1.1309
C 0.9997 -1.9155 0.1913
C 1.7285 1.8344 -0.7277
C 1.1437 0.9261 1.5588
C 3.1644 -0.6155 -0.2085
C -4.6490 0.7442 -0.6282
C 3.2525 1.9378 -0.4590
C 3.8298 0.5879 -0.2856
C 4.1654 -1.5888 0.0140
C 5.3604 -0.9015 0.0689
H -0.4604 0.5817 -1.5108
H -3.5646 0.2626 2.1897
H -1.0861 -0.4449 2.1498
H -2.1902 -1.7145 1.7003
H -2.5286 -0.2495 -1.7981
H -2.8534 -1.8505 -1.1460
H -0.3943 -2.1694 -1.4136
H -0.9135 -2.8938 0.0946
H -1.9810 2.0650 -0.9487
H -0.7587 2.7222 0.0818
H 1.5605 -0.7646 -1.4951
H -1.7642 1.9154 2.0477
H -3.1082 2.4431 1.0635
H 1.0176 -1.9046 1.2859
H 1.5276 -2.8282 -0.1118
H 1.2808 2.8061 -0.4944
H 1.5851 1.6842 -1.8068
H 0.5898 1.8173 1.8670
H 0.8147 0.0892 2.1727
H 2.1832 1.0992 1.8532
H -4.1337 1.6158 -1.0351
H -5.4265 1.0934 0.0595
H 3.4273 2.5264 0.4487
H 3.7385 2.4646 -1.2871
H -3.9519 -2.0832 0.7635
H 4.0442 -2.6573 0.1180
H -5.7603 -0.6874 -1.3370
H 6.3869 -1.2031 0.2186
"""
cafestol = vlx.Molecule.read_xyz_string(cafestol_xyz)
Show code cell source
kahweol_xyz = """49
kahweol initial structure
O -4.4710 -1.5361 0.0905
O -5.6188 0.9753 -0.0811
O 5.1625 0.5695 -0.0997
C -1.2209 -0.8317 -0.2017
C -0.4821 0.5357 -0.4703
C -3.0038 0.1167 1.0462
C -1.8514 -0.8737 1.1997
C -2.4967 -0.9058 -1.1119
C 0.9884 0.6333 0.0944
C -3.6676 -0.3924 -0.2474
C -0.3220 -2.0551 -0.4569
C -1.3919 1.7479 -0.1363
C -2.4167 1.5304 0.9816
C 1.7435 -0.6786 -0.3542
C 1.0741 -1.9483 0.1552
C 1.0367 0.8330 1.6293
C -4.5845 0.5870 -0.9677
C 1.7610 1.8511 -0.4907
C 3.2146 -0.5444 -0.1101
C 3.1013 1.8722 -0.6493
C 3.8167 0.6946 -0.3059
C 4.2309 -1.4546 0.2464
C 5.3980 -0.7259 0.2399
H -0.3415 0.5842 -1.5631
H -3.6779 0.0397 1.9072
H -1.1861 -0.6021 2.0159
H -2.2356 -1.8757 1.4322
H -2.3648 -0.3090 -2.0216
H -2.6844 -1.9384 -1.4328
H -0.2098 -2.1924 -1.5413
H -0.8043 -2.9694 -0.0890
H -1.9406 2.0033 -1.0514
H -0.8134 2.6482 0.0921
H -1.9341 1.7452 1.9434
H -3.2193 2.2709 0.8849
H 1.6699 -0.7251 -1.4553
H 1.0259 -1.9792 1.2481
H 1.6508 -2.8307 -0.1490
H 2.0514 1.0518 1.9842
H 0.4166 1.6762 1.9486
H 0.7233 -0.0489 2.1864
H -5.0524 0.1195 -1.8415
H -4.0679 1.4861 -1.3088
H 1.2088 2.7568 -0.7218
H -5.0925 -1.2746 0.7905
H 3.6240 2.7536 -0.9997
H 4.1386 -2.5085 0.4650
H -6.2132 0.2149 0.0339
H 6.4308 -0.9731 0.4374
"""
kahweol = vlx.Molecule.read_xyz_string(kahweol_xyz)
The difference between cafestol and kahweol is very subtle, essentially only one double bond and two H atoms.
We optimize structures and compare the initial and final geometries.
scf_drv = vlx.XtbDriver()
opt_drv = vlx.OptimizationDriver(scf_drv)
opt_drv.ostream.mute()
opt_cafestol_results = opt_drv.compute(cafestol)
opt_kahweol_results = opt_drv.compute(kahweol)
viewer = p3d.view(viewergrid=(1, 2), width=600, height=250, linked=True)
viewer.addModel(cafestol_xyz, "xyz", viewer=(0, 0))
viewer.addModel(opt_cafestol_results["final_geometry"], "xyz", viewer=(0, 0))
viewer.addModel(kahweol_xyz, "xyz", viewer=(0, 1))
viewer.addModel(opt_kahweol_results["final_geometry"], "xyz", viewer=(0, 1))
viewer.setViewStyle({"style": "outline", "width": 0.05})
viewer.setStyle({"stick": {}, "sphere": {"scale": 0.25}})
viewer.zoomTo()
viewer.show()
You appear to be running in JupyterLab (or JavaScript failed to load for some other reason). You need to install the 3dmol extension:
jupyter labextension install jupyterlab_3dmol
The initial and final structures are close so you may need to zoom in to see the subtle differences.